Damming and diverting river water alters the channel characteristics and natural flow regime. The change in biotic and abiotic factors results in dissimilar habitat conditions upstream and downstream of the barrage. Given the habitat dissimilarity and therefore resource availability, we hypothesized the dissimilarity in waterbird abundance and species diversity in the river habitat upstream and downstream of the barrage. The study was conducted on a 24 km stretch of Ganga River at Narora, Uttar Pradesh, India. This stretch overlaps with a Ramsar site as well as an Important Bird and Biodiversity Area (IBA). Bird sampling was done using transect count method for summer and winter season in 2017. The abundance was studied in relation to three habitat variables viz. channel depth, channel width and anthropogenic disturbances using Generalized Linear Model. A total of 140 species of birds were recorded. There was statistically significant difference in the abundance of waterbirds between upstream and downstream stretch in winter season (Mann-Whitney U, p < 0.05). During winters, migratory waterbirds especially ducks and geese occupied the deep water upstream of barrage, while the downstream was mostly occupied by terns and cormorants. Waterbird species diversity was higher in downstream during winters (Effective Number of Species=28; Shannon’s Index= 3.35) and higher in upstream during summer (Effective Number of Species=25, Shannon’s Index=2.87). Channel width, channel depth and anthropogenic disturbance influenced waterbird abundance in both the seasons (Generalized Linear Model; p < 0.05). The influence of channel depth varied with season for the upstream stretch.